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Cadmium in PDB 3rjl: Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)

Enzymatic activity of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)

All present enzymatic activity of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337):
1.5.1.12;

Protein crystallography data

The structure of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337), PDB code: 3rjl was solved by Y.Patskovsky, R.Toro, R.Foti, R.D.Seidel, S.C.Almo, New York Structuralgenomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.267, 116.114, 181.768, 90.00, 90.15, 90.00
R / Rfree (%) 22.2 / 29.2

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 47;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) (pdb code 3rjl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 47 binding sites of Cadmium where determined in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337), PDB code: 3rjl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 47 in 3rjl

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Cadmium binding site 1 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd539

b:43.3
occ:1.00
OE2 B:GLU343 2.2 42.0 1.0
OE2 A:GLU343 2.4 46.5 1.0
O A:HOH557 2.4 20.0 1.0
O A:HOH587 2.6 21.6 1.0
OE1 B:GLU343 2.6 27.2 1.0
OE1 A:GLU343 2.7 36.4 1.0
CD B:GLU343 2.8 39.8 1.0
CD A:GLU343 2.9 28.9 1.0
NZ A:LYS339 3.8 43.0 1.0
NE A:ARG340 4.0 51.2 1.0
CD B:ARG340 4.0 37.1 1.0
CD A:ARG340 4.1 28.0 1.0
CG B:GLU343 4.3 33.0 1.0
CE B:LYS339 4.3 34.4 1.0
CG A:GLU343 4.3 33.6 1.0
NH1 B:ARG340 4.5 43.0 1.0
CG A:LYS339 4.6 39.4 1.0
CZ A:ARG340 4.7 48.5 1.0
NE B:ARG340 4.8 35.9 1.0
CG B:LYS339 4.8 37.6 1.0
CE A:LYS339 4.9 46.8 1.0
NZ B:LYS339 4.9 26.8 1.0
CB B:GLU343 5.0 37.7 1.0

Cadmium binding site 2 out of 47 in 3rjl

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Cadmium binding site 2 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd540

b:88.4
occ:0.50
OD2 A:ASP393 3.0 55.3 1.0
OD1 A:ASP393 3.7 57.5 1.0
CG A:ASP393 3.8 59.6 1.0
NE2 A:GLN366 4.7 55.8 1.0

Cadmium binding site 3 out of 47 in 3rjl

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Cadmium binding site 3 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd541

b:86.9
occ:0.50
OE2 A:GLU352 2.1 72.2 1.0
OE1 B:GLU16 2.1 78.4 1.0
O A:HOH803 2.3 59.5 1.0
O B:HOH802 2.6 46.7 1.0
CD A:GLU352 3.2 71.8 1.0
CD B:GLU16 3.3 82.4 1.0
OE1 A:GLU352 3.7 68.9 1.0
OE2 B:GLU16 3.9 91.5 1.0
NZ A:LYS122 4.1 75.0 1.0
CG B:GLU16 4.3 72.2 1.0
CG A:GLU352 4.4 65.0 1.0
OD1 A:ASN30 5.0 83.7 1.0

Cadmium binding site 4 out of 47 in 3rjl

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Cadmium binding site 4 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd542

b:88.5
occ:0.50
OE1 A:GLU433 2.6 62.3 1.0
OE2 A:GLU433 2.6 59.2 1.0
CD A:GLU433 3.0 53.2 1.0
OG A:SER429 3.1 59.3 1.0
N A:SER429 4.0 53.5 1.0
O A:LYS427 4.1 45.3 1.0
CA A:VAL428 4.2 43.7 1.0
CB A:SER429 4.4 53.0 1.0
C A:VAL428 4.5 49.4 1.0
CG A:GLU433 4.5 46.8 1.0
CA A:SER429 4.9 53.0 1.0
CB A:VAL428 4.9 44.0 1.0
C A:LYS427 5.0 44.8 1.0

Cadmium binding site 5 out of 47 in 3rjl

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Cadmium binding site 5 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd543

b:72.3
occ:0.50
O A:HOH634 2.1 57.7 1.0
O A:HOH635 2.3 46.8 1.0
O A:HOH636 2.4 35.4 1.0
OD1 A:ASP432 3.7 66.4 1.0
CG A:ASP432 4.2 50.4 1.0
NE2 A:HIS456 4.6 28.4 1.0
N A:ASP432 4.6 37.1 1.0
OD2 A:ASP432 4.6 46.8 1.0
CB A:PHE431 4.8 39.1 1.0
CB A:ASP432 4.9 39.5 1.0
N A:PHE431 4.9 44.9 1.0

Cadmium binding site 6 out of 47 in 3rjl

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Cadmium binding site 6 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd544

b:76.5
occ:0.50
OD2 A:ASP455 2.7 66.6 1.0
OD1 A:ASP455 2.7 55.1 1.0
CG A:ASP455 3.0 52.9 1.0
CB A:ASP455 4.5 45.9 1.0

Cadmium binding site 7 out of 47 in 3rjl

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Cadmium binding site 7 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd545

b:81.0
occ:0.50
OXT A:ACT548 2.2 63.0 1.0
OE2 A:GLU224 2.8 68.4 1.0
OE1 A:GLU224 3.2 70.5 1.0
CD A:GLU224 3.4 64.6 1.0
C A:ACT548 3.4 69.1 1.0
NZ D:LYS108 3.4 56.9 1.0
O A:HOH579 3.5 43.6 1.0
O D:HOH799 3.6 38.0 1.0
CH3 A:ACT548 4.2 67.8 1.0
O A:ACT548 4.2 71.1 1.0
O D:HOH716 4.3 28.6 1.0
CE D:LYS108 4.8 52.7 1.0
NZ A:LYS108 4.8 37.9 1.0
CG2 A:VAL221 4.8 46.2 1.0
CG A:GLU224 4.9 50.3 1.0

Cadmium binding site 8 out of 47 in 3rjl

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Cadmium binding site 8 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd546

b:78.1
occ:0.50
OD1 A:ASP94 2.4 64.7 1.0
OD2 A:ASP94 3.0 69.9 1.0
CG A:ASP94 3.1 60.9 1.0
CG A:GLU96 3.4 57.6 1.0
CB A:GLU96 4.0 48.3 1.0
N A:GLU96 4.4 44.0 1.0
CB A:ASP94 4.6 51.3 1.0
CD A:GLU96 4.7 69.9 1.0
CA A:GLU96 4.8 46.2 1.0
OE1 A:GLU96 4.9 79.7 1.0
N A:PRO95 5.0 47.2 1.0
CD A:PRO95 5.0 44.0 1.0

Cadmium binding site 9 out of 47 in 3rjl

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Cadmium binding site 9 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd547

b:92.5
occ:0.50
OE1 A:GLU298 2.3 79.8 1.0
CD A:GLU298 3.1 75.8 1.0
OE2 A:GLU298 3.1 75.8 1.0
CG A:GLU298 4.5 63.0 1.0

Cadmium binding site 10 out of 47 in 3rjl

Go back to Cadmium Binding Sites List in 3rjl
Cadmium binding site 10 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd539

b:47.1
occ:0.50
O B:ACT543 2.0 56.5 1.0
O B:HOH801 2.3 63.0 1.0
OE2 B:GLU224 2.3 66.0 1.0
O B:HOH638 2.4 54.4 1.0
O B:HOH639 2.7 54.8 1.0
C B:ACT543 3.0 59.3 1.0
CD B:GLU224 3.1 63.2 1.0
OE1 B:GLU224 3.3 49.2 1.0
OXT B:ACT543 3.3 63.3 1.0
NZ B:LYS108 3.6 47.1 1.0
CH3 B:ACT543 4.3 57.4 1.0
O B:HOH800 4.4 32.9 1.0
NH1 B:ARG111 4.5 69.5 1.0
CD B:LYS108 4.5 44.6 1.0
CG B:GLU224 4.6 46.0 1.0
CG B:LYS108 4.6 39.8 1.0
CE B:LYS108 4.7 36.9 1.0
CB B:GLU224 4.9 39.5 1.0

Reference:

Y.Patskovsky, R.Toro, R.Foti, R.D.Seidel, S.C.Almo. Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis To Be Published.
Page generated: Sat Dec 12 08:23:05 2020

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